{"id":18810780,"url":"https://github.com/ecell/transomics2cytoscape","last_synced_at":"2025-04-13T20:31:09.994Z","repository":{"id":41067964,"uuid":"215441324","full_name":"ecell/transomics2cytoscape","owner":"ecell","description":"Get and integrate the pathways to create a 3D transomics network visualization","archived":false,"fork":false,"pushed_at":"2024-10-28T14:21:52.000Z","size":61533,"stargazers_count":5,"open_issues_count":0,"forks_count":0,"subscribers_count":9,"default_branch":"devel","last_synced_at":"2024-10-28T17:14:48.766Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ecell.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-10-16T02:41:53.000Z","updated_at":"2024-10-28T14:21:56.000Z","dependencies_parsed_at":"2023-09-24T16:45:16.218Z","dependency_job_id":"cea2347f-975b-4c62-8906-8c827da4c5a8","html_url":"https://github.com/ecell/transomics2cytoscape","commit_stats":{"total_commits":115,"total_committers":5,"mean_commits":23.0,"dds":"0.12173913043478257","last_synced_commit":"5b871a2180f2d9d45b58fa80c2a03a353405d775"},"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Ftransomics2cytoscape","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Ftransomics2cytoscape/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Ftransomics2cytoscape/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Ftransomics2cytoscape/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ecell","download_url":"https://codeload.github.com/ecell/transomics2cytoscape/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":223603545,"owners_count":17172117,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-07T23:22:21.328Z","updated_at":"2024-11-07T23:22:22.027Z","avatar_url":"https://github.com/ecell.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# transomics2cytoscape\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8201898.svg)](https://doi.org/10.5281/zenodo.8201898)\n\n[![BioC Release Build Status](http://bioconductor.org/shields/build/release/bioc/transomics2cytoscape.svg)](http://bioconductor.org/checkResults/release/bioc-LATEST/transomics2cytoscape/) - Bioconductor Release Build\n\n[![BioC Dev Build Status](http://bioconductor.org/shields/build/devel/bioc/transomics2cytoscape.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/transomics2cytoscape/) - Bioconductor Dev Build\n\n## Introduction\n\nVisualization of trans-omic networks helps biological interpretation by\nillustrating pathways where the signals are transmitted.\n\nTo characterize signals that go across multiple omic layers, [Yugi and\ncolleagues have proposed a method for network visualization](https://pubmed.ncbi.nlm.nih.gov/25131207/)\nby stacking multiple 2D pathways in a 3D space.\n\nThe 3D network visualization was realized by [VANTED](https://www.cls.uni-konstanz.de/software/vanted/).\nHowever, the visualization relies on time-consuming manual operation.\nHere we propose **transomics2cytoscape**, an R package that automatically creates\n3D network visualization in combination with\nCytoscape, [Cy3D App](http://apps.cytoscape.org/apps/cy3d), and\n[Cytoscape Automation](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1758-4).\n\n## Installation\n\n1. Install Cytoscape from https://cytoscape.org/\n2. Install transomics2cytoscape (see https://www.bioconductor.org/packages/release/bioc/html/transomics2cytoscape.html)\n\n## Example\n\n1. Run Cytoscape (If Cytoscape is already running, you don't need to run it anymore. transomics2cytoscape works only when 1 Cytoscape [window] is up.)\n2. Run R.\n3. Run the following R code. This will import multiple networks and integrate the networks to a 3D space. (This will take a few minutes.)\n\n```R\nlibrary(transomics2cytoscape)\nnetworkDataDir \u003c- tempfile(); dir.create(networkDataDir)\nnetworkLayers \u003c- system.file(\"extdata/usecase1\", \"yugi2014.tsv\",\n                            package = \"transomics2cytoscape\")\nstylexml \u003c- system.file(\"extdata/usecase1\", \"yugi2014.xml\",\n                            package = \"transomics2cytoscape\")\nsuid \u003c- create3Dnetwork(networkDataDir, networkLayers, stylexml)\n```\n\nNext Run the following R code. This will add edges between the network layers. (This code execution finishes faster than before.)\n\n```\nlayer1to2 \u003c- system.file(\"extdata/usecase1\", \"k2e.tsv\",\n                            package = \"transomics2cytoscape\")\nsuid \u003c- createTransomicEdges(suid, layer1to2)\nlayer2to3 \u003c- system.file(\"extdata/usecase1\", \"allosteric_ec2rea.tsv\", package = \"transomics2cytoscape\")\nsuid \u003c- createTransomicEdges(suid, layer2to3)\n```\n\nThen, you should have a 3D view with layered networks and transomic\ninteractions between them.\n(Note that you need to perform operations such as zooming out or adjusting the\ncamera angle.)\n\n![allosteric_result](man/figures/yugi2014.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fecell%2Ftransomics2cytoscape","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fecell%2Ftransomics2cytoscape","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fecell%2Ftransomics2cytoscape/lists"}